#!/usr/bin/env python
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
# pylint: disable=no-member
#
# @Author: oesteban
# @Date: 2016-01-05 11:33:39
# @Email: code@oscaresteban.es
# @Last modified by: oesteban
""" Encapsulates report generation functions """
from __future__ import print_function, division, absolute_import, unicode_literals
[docs]def individual_html(in_iqms, in_plots=None, exclude_index=0, wf_details=None):
import os.path as op #pylint: disable=W0404
import datetime
from json import load
from mriqc import __version__ as ver
from mriqc.utils.misc import BIDS_COMP
from mriqc.reports.utils import iqms2html, anat_flags, read_report_snippet
from mriqc.data import IndividualTemplate
from mriqc import logging
from io import open #pylint: disable=W0622
report_log = logging.getLogger('mriqc.report')
report_log.setLevel(logging.INFO)
with open(in_iqms) as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
fname = op.splitext(op.basename(in_iqms))[0]
out_file = op.abspath(fname + '.html')
if in_plots is None:
in_plots = []
if wf_details is None:
wf_details = []
# Extract and prune metadata
metadata = iqms_dict.pop('metadata', None)
mod = metadata.pop('modality', None)
file_id = [metadata.pop(k, None)
for k in list(BIDS_COMP.keys())]
file_id = [comp for comp in file_id if comp is not None]
pred_qa = metadata.pop('mriqc_pred', None)
# Deal with special IQMs
if mod in ('T1w', 'T2w'):
flags = anat_flags(iqms_dict)
if flags:
wf_details.append(flags)
elif mod == 'bold':
pass
else:
RuntimeError('Unknown modality "%s"' % mod)
config = {
'modality': mod,
'sub_id': '_'.join(file_id),
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict, 'iqms-table'),
'svg_files': [read_report_snippet(pfile) for pfile in in_plots],
'exclude_index': exclude_index,
'workflow_details': wf_details,
'metadata': iqms2html(metadata, 'metadata-table'),
'pred_qa': pred_qa
}
if config['metadata'] is None:
config['workflow_details'].append(
'<span class="warning">File has no metadata</span> '
'<span>(sidecar JSON file missing or empty)</span>')
tpl = IndividualTemplate()
tpl.generate_conf(config, out_file)
report_log.info('Generated individual log (%s)', out_file)
return out_file